Interesting. Seems that my rationing for how a transphasic torpedo worked is pretty much the same as everyone else's: It phases out of the space time continuum, then when it's reached it's pre-determined target, it phases back in and destroyes it.
My ONLY issue is when you see the torpedo hitting the cubes, there is a visible external explosion. This i can't explain unless it only partially phases out of the space time continuum, just enough to penetrate shields and armor, but just not enough to litterally tunnel it's way through the hull of the ship. This is possible if the hull of the torp is that gancy armor future janeway brought back.